I've just tried to update Nextcloud 18.03 and its security system found extra files. These seem to be non-nextcloud error files (e.g. 502.html etc) in /error/ directory and files from awstats in a /stats/ directory Are these from ISP Config and, if so, is it possible to move them out of the nextcloud webroot?
They are from ISPConfig. You can remove them but you'll have to disable statistics and custom error pages in ISPConfig.